Citation Management with Endnote Basil Marti Thüringer … · 2013-10-28 · What to expect?...

Citation Management with Endnote 22.10.2013/29.10.2013 Basil Marti Thüringer Universitäts- und Landesbibliothek

Thüringer Universitäts- und Landesbibliothek - Basil Marti

What to expect?

Introduction into the reference management software EndNote

Import, organization and usage of

bibliographic data

How are we proceeding?

1. Presentation & live demonstrations

2. Exercices

Thüringer Universitäts- und Landesbibliothek - Basil Marti 2

Workshop Overview

1. 09:00 – 13:00 (?)

2. Second part: 29 October, same time,

same room

Collecting bibliographic data by hand/on paper?

(1) Lots of effort

(2) Prone to errors

(2) Difficult to organize

Reference management software like EndNote offers:

1. Central database for bibliographic information

2. Automatic import of bibliographic data

Why reference management?

„In need to cite an article I read half a

year ago – but can’t find it again!

Citation management instead of chaos

Creating citations and bibliographies when writing papers/theses:

(1) Lots of effort

(2) Correct formatting is difficult

(3) How to avoid errors

Reference management software can do this automatically!

Why reference management?

Introduction & Installation

EndNote is a database program. The interface language is English.

EndNote helps

Collecting and organizing literature (bibliographic references, full-texts, abstracts, pictures, figures, tables …) and

Writing scientific works

EndNote is the most used Reference Management Software worldwide.

Competitors are Reference Manager, Citavi, ProCite, Mendeley, Zotero

Introduction (1)

Important Competitors:

• Citavi (www.citavi.com)

• Similar to EndNote

• Knowledge management functions

• Only for Windows

• FSU-licence

• Zotero (http://www.zotero.org/)

• Browser-plugin, plattform-independent, free

• Good for direct import of references into your database

• Mendeley (www.mendeley.com)

• Both online/offline versions, plattform-independent, free

• Social network functions for scientists

Introduction (1)

EndNote allows fast and easy entering of information from different online data-sources.

Web of Science (WoS)/ISI Web of Knowledge

PubMed

SciFinder

Biological Abstracts

Google Scholar

Electronic library catalogues (OPAC’s)

Introduction (2)

• Save references in a Library, which can be locally accessed and imported into commonly used word processors (WORD, OpenOffice.org, Apple Pages)

• References can be sent to

-> online reference management, sharing of libraries between different team-members.

• Collection of literature: unlimited amount of data entries

• Insertion of citations into your documents and automatic generation of bibliographies

• Great amount of formatting styles (>5550 Output Styles)

Introduction (3)

• Producer: Thomson Reuters

• Thomson Reuters:

Producer of Web of Science (WoS, Web of Knowledge), EndNote & EndNote Web

• EndNote and EndNote Web are integrated into WoS and optimized for use with WoS

• EndNote Web can be used for free for subscribers to WoS (-> free for university members and students of the FSU)

Introduction (4)

• Windows

• Windows XP, Vista, 7, 8

• Macintosh

• Mac OS X 10.6 and later

• Word Processors (Windows)

• Microsoft Word 2007, 2010, 2013

• Microsoft Power Point 2013

• Open Office 3.X

• RTF files

• Word Processors (Mac)

• Microsoft Word 2008, 2011

• Apple Pages 09

System requirements (1)

• State licence agreement offers access (minimal duration till 30.11.13)

FSU-organisations: Installation via Rechenzentrum; softwarebeschaffung@uni-jena.de

Staff and students (HomeUseLicence)

a. Free use at home/private computers

b. Download: www.tu-ilmenau.de/unirz/EndNote-X-4-0-2.4952.0.html

c. Download is only possible using the IP-range of Thuringian universities

d. Accept licence agreement (Nutzungsbedingungen)

Installation (1)

• Installation: extract zip file completely, install on your local computer

• Installation modi:

1) Automatic Installation: Installation of the 100 most important citations styles

2) Manual installation: Installation of additional Life Sciences Styles recommended.

• Additional styles can be imported at a later date

1) EndNote Style Collection: http://www.endnote.com/support/enstyles.asp

More than 5500 Output Styles

Sorting options

Installation (2)

First Steps & References

• Create a new library using the File/New menu option

• Open an existing library using File/Open

• Database file format: .enl („EndNote Library“)

• .data folder with full texts etc.

First steps: Creation of an Endnote library

EndNote Libraries consist of two components: .enl and .data.

User interface Thüringer Universitäts- und Landesbibliothek - Basil Marti

Menu and tool bars with common commands, e.g. import, online search, insert into Word etc.

Group-overview and activities Display Fields

Output-preview

Search window

Display Fields – bibliographic metadata

Column bar with up to 10 colums (Clicking on collums sorts entries)

Edit Colums using Edit / Preferences / Display Fields

Display fields– individual ratings

Sort by „read“ and „unread“

Individual Rating: Zero till 5★ possible

Detail view (double click on reference)

Fields

Reference type

Rating

Modify reference types

• It is possible to create new reference types and modify existing ones: Edit/Preferences/References Types

Keywords

• Keywords are possible for all reference types

• Recommendations

Individual tagging of references

Rating of references with e.g. „very important”, „discussion“, „introduction“ etc. allows for fast rediscovery at a later date

Term lists

Manage keywords with term lists: Tools/Open Term Lists Define list of pre-defined keywords Also available for other fields (e.g. author, journal)

Enter, search and import

Manual data entry

Search in local EndNote libraries

Online search in different databases

Endnote import functions

Search for full texts

Online Search

• Search and import using the online-mode of EndNote

Import data – 6 possible ways

Direct export from online databases and catalogues

• Search in an external database

• Use the Save/Export function

• EndNote starts automatically

• E.g.: WoS

Manual data entry

• Create new reference

• Select reference type

• Fill in metadata by hand

• Add figures and pdf-files

Import of text files

• Save/Export as text file

• Import in Endnote

• Select import filter

Import data – 6 possible ways

Import of pdf-

• Metadata of pdf-files are automatically inserted as an Endnote reference and linked to the pdf-file

From EndNote Web

• Synchronisation

• Select New Reference in the toolbar:

• Enter data by hand

• Hints: Enter personal names as “first-name surname” or “surname, first-name”. Add a new line for additional authors/contributors

• Add a new line for several keywords

• Avoid line breaks in title or other fields

• Attention: Manual data-entry is time-consuming and error-prone: If possible use an online source and import the metadata (bibliographic databases for article, library catalogues for books)

Manual data entry

Search in local EndNote libraries

3 search modes

Integrated Library & Online Search

Local + Online

Default

Online search results are loaded directly into your own library (All References)

Online Search Mode

Online

Only online search

Add search results into library by selecting Copy to Local Library

Local Library Mode

Search only in the local library

3 search modes

Integrated Library & Online Search

Online Search Mode

Local Library Mode

Edit your references using the Local Library Mode

When searching in databases with EndNote, use the Online Search Mode

If possible avoid the Integrated Library & Online Search Mode.

Quick Search & Library Search

Search the local library(1)

• Save/Load searches

• Search the whole library or subsets

• Automatic truncation (left and right)

• Match Case and Match Words: exact search

• Boolean operators: AND, OR, NOT

Operator Bedeutung

AND Both conditions have to be true

OR One of the condition has to be true

NOT The condition has to be false

• Search for keywords or ratings is possible

• Can be used to create smart groups

Search in the local library(4)

Online search – Search in external databases

(1) Links (=Connection Files) are available for many databases

• PubMed

• Web of Science

• GeoRef

• Biological Abstracts

• ThULB library catalogue (OPAC)

(2) Add database using Tools / Online Search... / PubMed )

(3) Database appears in the group Online Search

Online search in EndNote (1)

Drawback: Limited search options

- Detailed options when searching directly in the database make the online search inside EndNote only the second choice

- Search results are deleted after closing EndNote

Online Search-Fenster

Tip: Review search results by selecting Show All Fields and the Preview tab

Direct Export from Online-Databases

Almost all bibliographic online-databases have an export function. E.g.:

• Web of Knowledge (Web of Science, WoS)

• PubMed

• Ovid databases

• EBSCO Host databases

• Google Scholar

• KVK (Karlsruher Virtueller Katalog)

Direct Export

• WoS is an interdisciplinary portal

• Range of subjects: Medicine, Science, Social Sciences, Technology, Humanities and Art

• 10 000 scientific journals indexed with ca. 37 million indexed articles

Direct export from WoS (1)

(1) Search in WoS

(2) Click Button Save to EndNote

(3) Select Open with ResearchSoft Direct Export Helper (default value)

(4) Reference is automatically opened in Endnote and moved into the group Imported

(5) Import pdf-files using the Find Full Text function

Direct export from WoS (2)

EBSCO Host is a provider (=search interface) for different scientific databases, for example

• PSYNDEX

• Business Source Premier

• EconLit

• Historical Abstracts

• L'Année philologique

Export from EBSCO Host databases

(1) Intermediate storage of references in Folder

(2) Export button

(3) Export as a ris-file

(4) Can be opened with EndNote

Export from EBSCO Host databases

• OvidSP is a database provider offered by Wolters Kluwer

• It allows for access to databases like

• Biological Abstracts

• INSPEC

• Philosophers Index

• GeoRef

Export from Ovid databases

(1) Select search results

(2) Select Export

(3) Open the generated cgi-file

with Endnote

Export from Ovid databases

PubMed contains the medicinal database MEDLINE, which indexes 4600 biomedical journals and e-books and contains ca. 21 million citations.

PubMed

(1) Select search results

(2) Send to - Citation Manager - create file

(3) Select Open with EndNote X7

(4) Search results are imported

Export from PubMed

SciFinder is the biggest information resource for chemistry and related fields. It contains 34 million references from 10 000 journals, patents, books, conference proceedings and dissertations. Additionally, it offers information about 70 million chemical substances and 63 million protein/nucleotide-sequences

SciFinder (Chemical Abstracts)

1. Select search results and choose Export

2. Export as ris-file

3. Open ris-file with EndNote

SciFinder

(1) Export is only possible for single search results

(2) Activate export to EndNote in the Google Scholars settings

Export from Google Scholar (1)

(1) Select Import into Endnote

(2) Open the enw-file with Endnote

Export from Google Scholar (2)

• Helpful tool

• Import a single pdf file or a folder containing pdf files

• EndNote automatically „unpacks“ the pdf and adds

• Bibliographic data

• Attachment (PDF) / Full text

Metadata extractions only works when the pdf file contains a DOI (Digital Object Identifier)

Import pdf files

• File/Import File or File/Import Data

• Select Import Option: PDF

Import pdf-files

Fulltexts

(1) Save pdf file locally

(2) Paper clip button or References/File Attachements/Attach File

(3) Paper clip symbol appears in the display

(4) pdf is attached

(5) pdf is stored in the EndNote data folder: /user/documents/MyEndnotelibrary.Data/

Attach pdf files (1)

• An unlimited number of pdf files can be attached to a single reference

• Multiple functions: Print, Save, Notes, Turn, Highlight, Full text

• Open pdf file with external viewer:

• Mail pdf file:

Attach pdf files (2)

Nr. 13

• pdf files can be highlighted and commented inside the EndNote pdf viewer

• Note: Annotations and highlighted text are only visible inside EndNote -> does not appear when opening the pdf file with another reader

Pdf highlighting and annotations

Create links between references and different files, e.g.:

(1) Pdf fulltext as attachment

(2) Image

(3) PowerPoint-file

(4) Excel file

(5) Diagram

(6) URL

Using the detail view:

References/File Attachments/Attach File or

References/Figure/Attach Figure

Create links (1)

Add a figure by clicking the pin button

Attachment appears in the field figure

Create links using the pin button

• Works best when the IP-range of the University

• Tip: If EndNote fails to find a full text, search manually using the EZB (Elektronische Zeitschriftenbibliothek) or other search tools

1. Select reference(s)

2. Find Full Text (context menu) oder

3. Found full texts are listed in the Found PDF group

Find full text

OpenURL is a service which checks for full text in the electronic ressources licensed by the university library. It can be activated in EndNote in order to improve the sucess of the Check Full text function.

Activate OpenURL (ThULB Linker) service in EndNote:

a. Edit / Preferences / Find Full Text

b. Activate all possible options

c. Enter URL for the path to the ThULB-Linker: „http://yq5uk2ps4v.search.serialssolutions.com“ in the field OpenURL Path

OpenURL Link

(1) Select reference

(2) Select URL/OpenURL Link in the Context menu

(3) Results are shown in browser window

Use OpenURL Link manually

Reference Organization

My Library

• Organization of EndNote libraries • Categorization of references according to

different criteria

(1) Permanent groups All References and Trash are always

shown (2) Temporary groups

Automatically generated when executing certain commands

Deleted when closing EndNote or the library

E.g. Imported, Unfiled

My Library

(3) User defined groups Custom groups Smart groups Groups created from groups

(4) Online search Results of Online-searches from

EndNote Overwritten when executing a new

search Possible with lots of different

databases (=Connection Files)

Groups are subsets of the total set of (All References).

Groups appear under My Groups in the group window

Groups are created individually

Grouping of references (Groups)

• Thematical groups

• Recommended when writing scientific papers

Introduction

Materials/Methods

Discussion

Subject 1

Subject 2

• References of an author

• References of a workgroup

Grouping of references (Groups)

(1) Custom Groups

Defined, fixed groups

Manual assignment

Grouping of references (Groups) (2)

(2) Smart Groups

Dynamic groups

Based on search queries

Automatically updated

(3) Groups created from groups

Combination of other groups (both custom and smart groups)

Combination based on boolean operators: union, intersection or complement of sets

Grouping of references (Groups) (3)

Creation of Custom Groups

• Select reference(s)

• Right mouse button

• Add References To / Create Custom Group

• Right mouse button

• Create new group

• Enter name

• Adding references with drag and drop

• „Intelligent “ groups

• Dynamically generated

• Use with keywords: E.g. sort by „very important“, „important“

• Another possible use: Create a group with all references by a certain author

• Can be created in different ways

Smart Groups

(1) My Groups / Create Smart Group

(2) Search window appears

(3) Enter search queries used to define the smart group

(4) Name group

Create Smart Groups (1)

Different way:

•In the search window of the library

(1) Start search

(2) Options / Convert to Smart Group

(3) Enter group name

Create Smart Groups (2)

Right-click in the group window: Create from Groups…

•Select

(1) Group name

(2) Secect groups to combine

(3) Define boolean operators

Create Groups from groups

• Higher-level groups • Contain individual groups (both custom and/or smart

groups)

Create group sets(1)

(1) Menu My Groups / Create Group Set

(2) Name Group Set

(3) Fill Group Set by Creating new groups or by drag-and-dropping existing groups

• The Unfiled group contains all references which are not part of a different groups

Note: To check which groups a reference is part of, select the reference and choose Record Summary in the context menu. References can be part of multiple groups.

Create Group Sets (2)

Delete groups and references

Delete groups

• Deletes groups, but not the references

• Cannot be undone!

Delete references

from Custom Groups

Only group membership is deleted

References is still availble under „All References“

from Smart Groups/Group from groups

Reference is moved to the trash!

Restore references into smart group is possible(Restore to Library)

Edit / Preferences / Duplicates

Find duplicates (1)

Edit default values

Control for duplicates is automatically applied with the default values

(2) References / Find Duplicates

• Compare potential duplicates (differences in blue)

• Select which record should be kept

Find duplicates (2)

Merge two databases

(1) File / Import File

• Select import option EndNote Library

• Prevent creation of duplicates by choosing Discard Duplicates

Export and Publication

Export libraries

Cite While You Write (CWYW) & WORD

Edit Citation styles (output styles)

Export libraries

• File/Export

• Output style

• EndNote Export for export to other citation management software

• BibTeX Export for LaTeX users

Export libraries

Cite While You Write (CWYW)

• Dynamical export of citations

in WORD

in other word processors

• Automatic generation of bibliographies

• Many different formats possible

• Insert citations from both WORD and EndNote

• Citations and bibliographies are dynamic: Style can be changed at any moment

Both WORD and the EndNote Library have to be open!

Close all non-necessary libraries

Cite While You Write (CWYW)

• Installation of an EndNote Plugin in WORD

• Adds EndNote X7-ribbon

Cite While You Write in WORD

(1) Insert Citation / Find Citation

(2) Search windows opens

(3) Search library by

(1) Author

(2) Keywords

(3) Journal name …

(4) Select reference and click on Insert

(5) Citation and bibliography entry are generated

Additional options when inserting references:

• Selecting and inserting multiples references

Additional options when inserting references:

• Insert & Display as: Author (Year): For use when mentioning the author in the running text. E.g. John Smith et al. (Citation) postulate that …

• Insert in Bibliography Only: No citation is inserted, reference is only included in bibliography

(1) Insert footnote

(2) Move cursor to footnote

(3) Insert Citation / Find Citation

Some citation styles are not

recommended for use with

footnotes!

Create Footnotes in WORD

(1) Move Cursor in Word to desired position

(2) Chance to EndNote

(3) Select reference in EndNote and click on Insert Citation

Cite While You Write in EndNote

The citation style can be changed at every time by using the drop down menu in Word. Citations and bibliography are then reformatted automatically.

Change citation style

(1) Select Insert Figure

(2) Select Figure or picture from list

(3) Figure is inserted with caption

Note: Figures and captions are not automatically updated when the EndNote library changes

Depending on the citation style, figures are inserted at the end of the document or in the main text

Insert figures & pictures

This function converts all citations and the bibliography to plain text, which you can edit with Word.

Use this function if you share your document whith someone who doesn‘t have you EndNote library or to manually edit citations or bibliographies.

Convert to plain text

• Sorting the bibliography to according to document types or customized criteria (e.g. primary/secondary sources or sources/further reading)

• Can also be used to create bibliographies for each chapter

Structured bibliographies

• Powerpoint

• Insert Citation: (Martin de las Mulas et al., 2002)

• Insert Reference: Martin de las Mulas, J., Espinosa de los Monteros, A., Bautista, M. J., Gomez-Villamandos, J. C., & Morales, C. (1994). Immunohistochemical distribution pattern of intermediate filament proteins and muscle actin in feline and human mammary carcinomas. J Comp Pathol, 111(4), 365-381.

• No bibliography in available in PowerPoint document

• No dynamic formatting: Insertion as plain text

Other programs

Edit citations styles (output styles)

• Select style in the EndNote drop down list

• Select a reference

• Preview is shown in the Preview Tab

Style preview

• Endnote offers more than 5500 output styles for formatting citations and bibliographies

• File Format: *.ens (EndNote Styles)

• The standard installations only contains the 100 most popular styles

• Additional styles can be downloaded: http://www.endnote.com/support/enstyles.asp

Output styles

• Search for specific styles and download on the EndNote website

Output Styles

• Edit / Output Styles / Output Style Manager

• Create an individual style:

(1)Select an existing style as starting point:

Style Info Preview

& Edit

(2)Edit & save style

Output Style Manager

• Check for style recommendations/regulations of your journals/university/institute/supervisor

• Edit different categories

a. Citations

b. Bibliography

c. Footnotes

d. Figures & Tables

Edit style

Citations

Bibliography

Footnote

Figures & Tables

Edit style

• In-Text Citations

(1) Templates

(2) Insert Field

e.g.: Author, Year. Add commas or semicolons by Hand

Edit citations

• Author Lists/Author Name: How/how many authors are shown in citations

Edit citations

• Define bibliography pattern

• Add new reference types

Online Database

Personal

communication…

Edit bibliography(1)

Enter fields using the Insert Field button.

Enter special characters (e.g. commas, parentheses) by hand

Edit bibliography (2)

Important rules:

• Dependance: Characters or Punctuations which are directly connected to an EndNote field (e.g. author) are only shown if the field is not empty

• |(Forced Separation): Ignores Dependance (e.g. author|,)

• non breaking space (diamond symbol): joins two parts together, creates dependance

• ^: Singular/Plural forms (e.g. (Ed.)^(Eds.))

Sort order of the bibliography

Three possibilities to determine the footnote style:

• Define your own templates

• Use formatting of bibliography entries

• Use formatting of citations

Edit footnotes

• Placement of figures and tables

In the text

At the end of the document

Placement of the caption

Edit Figures & Tables

(1) Exit Output Style Manager:

(2) Save changes

(3) Tip: Save the edited style under a new name

Save style changes

Online & Collaborative reference management

Teamwork

Compressed Library

Copy database

Static

File / Save a Copy

Data folder not included

EndNote using a

network

EndNote Web

Static

*.enlx

File / Compressed Library

File / Open / Open Library

Send by mail

(Dynamic)

Work on a joint network drive

Read-only

Dynamic

Synchronize and share data:

(1) For Backup-purposes (Recommended!)

(2) For collaborative work

• Send by mail is possible

• Compressed format

• Save with/without attachments

(1) File / Compressed Library

(2) Save locally

(3) Open with File / Open / Open Library /… .enlx

Compressed Library

EndNote on a network drive

Read-ony copy of the database on the local network drive

Administrator-data

management

Intellectual legwork of the colleagues (e.g. mailing of pdf)

• Bidirectional synchronization between EN Desktop- und Online-Version

• Access from everywhere using a web browser

• Menus in different languages (English/German etc.)

• EndNote Web is well suited for collaborative work

Teamwork and mobile work with EndNote Web

Disadvantages:

• Limited functionality

• No access to web-based libraries after leaving the institution licensing Endnote Web

• Account will be deleted after 1 year of inactivity

• No offline-editing possible

• More interference-prone (server problems, maintenance, stability of the internet connection)

Check first which functionalities are necessary for you!

EndNote Web

• One-time registration under

https://www.myendnoteweb.com/

• Download of word plugin for CWYW-editing possible

Registration of EN Web

Basic Functions of Endnote Web

References and groups

Groups

Edit reference

Attachements

Online Search:

Data entry or data import

(1) Synchronization

• Adding references

• Deleting references

• Editing references

• Only custom groups are synchronized

• Synchronization can only be started from EN Desktop

Synchronization EN Desktop and Web

(2) Up to 5 GB of space

(3) Rules for attachments

• All attachments will be synchronized in both directions

(3) Rules for deletion of attachments

• Deleted attachments will be synchronized again, if there are only deleted in one place

• In order to really delete an attachment the attachment has to be manually deleted both in EN Desktop and Web.

Synchronization EN Desktop and Web

(1) Edit /Preferences / Sync / Enable Sync

Synchronization with Endnote Web

Computer A Computer B Situation Two different computers

Select group for collaborative editing

Mutual adding of email-adresses

Allow read-only or read&write acess

EndNote Web – Collaborative work

129 Thüringer Universitäts- und Landesbibliothek - Basil Marti

• Select group • Enter e-Mail adresses • Option: Read only /

Read & Write

130 Thüringer Universitäts- und Landesbibliothek - Basil Marti

• No sharing of attachments • Shared groups are only synchronized for the original

owner of the group, not for the invited collaborators

Information and Support

Additional informations in the Internet

• http://www.endnote.com/

① EndNote Homepage

② User Forum

③ Technical Support

④ Online Tutorial – always available

⑤ Webinar (live) with different subjects

⑥ Handbook in different languages (both German and Englisch)

• http://www.adeptscience.de/bibliographie/endnote/index.html (German distributor)

① Technical questions

② Handbook in different languages (both German and Englisch)

③ German webinars (gratis)

Additional support

Questions?

Basil Marti ThULB

Tel.: 9 40036

basil.marti@thulb.uni-jena.de

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Citation Management with Endnote Basil Marti Thüringer … · 2013-10-28 · What to expect?...

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